Save window layout instead of startup file?
The window layout(s) of the blender scenes are saved as part of the file. Any file you open will ordinarily open with the window layout with which it was saved, unless when you select a file to open in the file browser window, you make certain that the box beside "load UI" in the options pane (customarily to the left of the screen) is unchecked. If you are starting from your default custom startup window arrangement, and unchecked the "load UI" box, the file you load will be in your customized window arrangement. And once you save the file from this arrangement,  when you re-open the file, it will be in your desired window layout.